I agreed with a format if you just want to start over but formatting will never fix your games.
To fix internal hard drive games your options are:
Backup your app.db and restore it (doesn't appear you did this)
Run the python script (you won't be able to delete any of your games without editing app.db)
To fix external hard drive games:
Unplug external
Run Goldhen
Replug external
Wait a little while for the games to load and reappear
Neither of these scenarios require a format. Formatting literally means I'm giving up and starting over because you're erasing all data on that hard drive and Hen cannot save it after that
This is the correct python script for 9.0 (if internal games are missing)
https://github.com/aizenar/PS4_db_Rebuilder_EXT